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pysam

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About pysam

P

pysam

Provides Python/HTSlib workflows for genomic files

pysam is an agent skill for low-level, streaming access to genomic files through HTSlib, using the pysam Python package. It covers AlignmentFile and AlignedSegment for SAM, BAM and CRAM files, VariantFile, VariantHeader and VariantRecord for VCF and BCF files, FastaFile for indexed FASTA, FastxFile for sequential FASTA and FASTQ, and TabixFile for BGZF-compressed, tabix-indexed BED, GFF, GTF and custom tables. It also wraps the samtools and bcftools command-line tools through dispatchers. The current upstream baseline is pysam 0.24.1, released on 7 September 2026, which wraps HTSlib, samtools and bcftools 1.24. The skill tells you to read its source reference before updating version-specific guidance. For reproducible work you install a pinned release. Use it when you need to read, query, filter or write sequence alignments, variant calls or indexed annotation files from Python. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.

View pysamAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/pysam